PCR Assembly Primer Design
primerize.wrapper
Module¶primerize.wrapper.
Design_Plate
(init_dict)¶Bases: object
Result of a primerize.Primerize_2D.design()
or primerize.Primerize_3D.design()
run.
Parameters: |
|
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sequence
¶str
: Sequence of assembly design.
name
¶str
: Construct prefix/name.
is_success
¶bool
: Flag for whether a solution is found.
primer_set
¶list(str)
: Strings of solution primers.
structures
¶list(str)
: Strings of input secondary structures.
_params
¶Input parameters, in format of dict: { 'offset': int, 'which_muts': list(int), 'which_lib': list(int), 'N_PRIMER': int, 'N_PLATE': int, 'N_CONSTRUCT': int, 'N_BP': int, 'type': str }
.
For primerize.Primerize_3D.design()
results, it also has 'N_MUTATION': int, 'is_exclude': bool, 'is_single': bool, 'is_fillWT': bool
.
_data
¶Data of assembly solution, in format of
dict: {
'constructs': primerize.Construct_List,
'plates': list(list(primerize.Plate_96Well)),
'assembly': primerize.Assembly,
'illustration': { 'labels': list(str), 'fragments': list(str), 'lines': tuple(str) },
}
For primerize.Primerize_3D.design()
results, it also has 'bps': list(tuple(int, int)), 'warnings': list(tuple(int, int))
.
__repr__
()¶Representation of the Design_Plate
class.
__str__
()¶Results of the Design_Plate
class. Calls echo()
.
echo
(key='')¶Print part(s) of result in rich-text.
Parameters: | key -- |
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Returns: |
|
Raises: |
|
get
(key)¶Get result parameters.
Parameters: | key -- str : Keyword of parameter. Valid keywords are 'offset' , 'which_muts' , 'which_lib' , 'N_PRIMER' , 'N_PLATE' , 'N_CONSTRUCT' , 'N_BP' , 'PRIMER' , 'CONSTRUCT' , ('is_exclude' , 'is_signle' , 'is_fillWT' , 'STRUCTURE' and 'WARNING' only for primerize.Primerize_3D.design() results); case insensitive. |
---|---|
Returns: | value of specified key. |
Raises: | AttributeError -- For illegal key. |
save
(key='', path='./', name=None)¶Save result to text file.
Parameters: |
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Raises: |
|
primerize.wrapper.
Design_Single
(init_dict)¶Bases: object
Result of a primerize.Primerize_1D.design()
run.
Parameters: |
|
---|
sequence
¶str
: Sequence of assembly design.
name
¶str
: Construct prefix/name.
is_success
¶bool
: Flag for whether a solution is found.
primer_set
¶list(str)
: Strings of solution primers.
_params
¶Input parameters, in format of dict: { 'MIN_TM': float, 'NUM_PRIMERS': int, 'MIN_LENGTH': int, 'MAX_LENGTH': int, 'N_BP': int, 'COL_SIZE': int, 'WARN_CUTOFF': int }
.
_data
¶Data of assembly solution, in format of
dict: {
'misprime_score': [str, str],
'warnings': list(tuple(int, int, int, int)),
'assembly': primerize.Assembly
}
__repr__
()¶Representation of the Design_Single
class.
__str__
()¶Results of the Design_Single
class. Calls echo()
.
echo
(key='')¶Print part(s) of result in rich-text.
Parameters: | key -- |
---|---|
Returns: |
|
Raises: |
|
get
(key)¶Get result parameters.
Parameters: | key -- str : Keyword of parameter. Valid keywords are 'MIN_TM' , 'NUM_PRIMERS' , 'MIN_LENGTH' , 'MAX_LENGTH' , 'COL_SIZE' , 'WARN_CUTOFF' , 'WARNING' , 'PRIMER' , 'MISPRIME' ; case insensitive. |
---|---|
Returns: | value of specified key. |
Raises: | AttributeError -- For illegal key. |
save
(path='./', name=None)¶Save result to text file.
Parameters: |
|
---|
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Last updated on Jun 22, 2017.